chr14-24625650-C-T

Variant names:

• chr14-24625650-C-T
• rs11629129
• ENST00000555300.1:n.177+2524C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000555300.1(ENSG00000258657):​n.177+2524C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,300 control chromosomes in the GnomAD database, including 555 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.084 (555 hom., cov: 33)
• Consequence: ENSG00000258657 ENST00000555300.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 7 publications found

Genes affected

ENSG00000258657 (HGNC:58166):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258657	ENST00000555300.1	n.177+2524C>T		intron_variant	Intron 2 of 3	5
ENSG00000258657	ENST00000557736.5	n.439+2524C>T		intron_variant	Intron 2 of 2	4
ENSG00000258657	ENST00000770595.1	n.234+2524C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0836 AC: 12725 AN: 152182 Hom.: 550 Cov.: 33

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0760

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0741

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.0951

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0836 AC: 12737 AN: 152300 Hom.: 555 Cov.: 33 AF XY: 0.0825 AC XY: 6143 AN XY: 74468

African (AFR) AF: 0.0673 AC: 2795 AN: 41560

American (AMR) AF: 0.0669 AC: 1023 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0760 AC: 264 AN: 3472

East Asian (EAS) AF: 0.0611 AC: 317 AN: 5190

South Asian (SAS) AF: 0.132 AC: 637 AN: 4828

European-Finnish (FIN) AF: 0.0741 AC: 787 AN: 10622

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0970 AC: 6595 AN: 68006

Other (OTH) AF: 0.0937 AC: 198 AN: 2114

Alfa AF: 0.0959 Hom.: 1288

Bravo AF: 0.0816

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11629129; hg19: chr14-25094856;